{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-12T10:42:17Z", "providers": [ "Codex" ], "breadth": "recalled by Codex without web access - no source was read", "missingProviders": [], "pass": 2, "cost": { "grok": { "seconds": 22.4, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09534-fc06-7f33-a76b-ca00d2977ce0\n--------\nuser\nDescribe what is already known about one registered thing. Answer as JSON only, no prose around it.\n\nThing: kainate receptor\nSense to describe: (none recorded)\nDomain code: PHY.MAT\nAlso known as: (none)\n\n\nContext for this batch of 1001 things:\n# Batch 043: 100", "usd": 0.0, "recall": true }, "codex": { "seconds": 65.7, "error": "Reading additional input from stdin...\nOpenAI Codex v0.153.4\n--------\nworkdir: R:\\02_PROJECTS\\02_Meta_Models_Platforms\\Ver.cy\\current\\thing-registry-backlog\nmodel: gpt-6-astra\nprovider: openai\napproval: never\nsandbox: read-only\nreasoning effort: none\nreasoning summaries: none\nsession id: 01a09534-fbf5-7863-b05a-7afb4f821e40\n--------\nuser\nYou are drafting a Vercy meta-model for one registered thing. Answer as JSON only, no prose around it.\n\nThing: kainate receptor\nRegistry id: vr.tr.kainate-receptor\nPlane / domain: PHY / PHY.MAT\nRegistry definition: (none recorded)\nNames folded into this entry:" } }, "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T12:00:00Z", "ingestedAt": "2026-10-06T08:44:48+00:00", "fields": [ "agent_conduct", "ethics", "failure_modes_and_hazards", "owners", "standards_and_regulation" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:30+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q3454536", "registryId": "vr.tr.kainate-receptor", "name": "kainate receptor", "version": "0.1.0-research.1", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q3454536/", "model": { "registry_id": "vr.tr.kainate-receptor", "name": "kainate receptor", "purpose": "Enable an AI agent to identify a kainate receptor assembly, assess its functional state, and select interpretable measurements or experimental perturbations.", "definition": "A kainate receptor is a tetrameric ionotropic glutamate receptor assembled from GluK1-GluK5 subunits that mediates glutamate-activated cation conductance and modulates synaptic transmission in the nervous system.", "scope_statement": "This model owns vr.tr.kainate-receptor as a family of glutamate-gated receptor protein complexes in PHY / PHY.MAT, including their composition, membrane context, channel behaviour and receptor-specific interactions; individual subunits and experimental preparations are represented as related entities.", "in_scope": [ "GluK subunit composition, assembly and molecular variants", "Receptor membrane localization and associated proteins", "Ligand binding, activation, desensitization and recovery", "Ion permeation and electrophysiological properties under recorded conditions", "Pharmacological responses and evidence attributing an observed effect to kainate receptors" ], "out_of_scope": [ "Kainic acid, glutamate and other ligands as chemical substances", "GRIK genes and their transcriptional regulation as independent entities", "AMPA, NMDA and metabotropic glutamate receptor families", "Whole-neuron, synaptic circuit and organism models", "Disease diagnosis, treatment recommendations and clinical drug dosing" ], "distinguishing_features": [ "Identify the complex through GluK-family subunits; a response to kainate alone is insufficient to establish receptor identity.", "Distinguish an assembled receptor from a GRIK gene, transcript or isolated GluK protein.", "Check assembly compatibility: GluK4 or GluK5 alone does not establish a functional channel; these subunits require partners from GluK1-GluK3. [IUPHAR/BPS](https://doi.org/10.2218/gtopdb%2Ff75%2F2019.4)", "Distinguish ion conduction through the receptor from downstream signalling attributed to receptor activation.", "Separate ligand-bound desensitized receptors from open channels; ligand occupancy does not by itself demonstrate current flow." ], "characteristics": [ { "name": "Subunit composition", "kind": "relation", "unit_or_values": "GluK1-GluK5 identities, copy numbers where established, species and protein accessions", "why_it_matters": "Defines the assembly being assessed and constrains its possible functional properties." }, { "name": "Sequence and processing variants", "kind": "category", "unit_or_values": "Splice isoform, Q/R editing status where applicable, mutations, tags and unknown status", "why_it_matters": "Prevents functional results from being transferred indiscriminately between molecular variants." }, { "name": "Associated auxiliary proteins", "kind": "relation", "unit_or_values": "NETO1, NETO2, other experimentally supported partners, absent or untested", "why_it_matters": "Allows properties to be assigned to the measured receptor complex and its associated proteins." }, { "name": "Membrane localization", "kind": "state", "unit_or_values": "Intracellular, surface, presynaptic, postsynaptic, extrasynaptic or unresolved", "why_it_matters": "Distinguishes protein expression from availability to extracellular ligand and local signalling." }, { "name": "Functional channel state", "kind": "state", "unit_or_values": "Resting, activated/open, desensitized, blocked or unresolved", "why_it_matters": "Supports interpretation of current loss and subsequent recovery." }, { "name": "Ligand response parameters", "kind": "measurement", "unit_or_values": "EC50, IC50 or Kd in mol/L; efficacy relative to a named reference; assay conditions required", "why_it_matters": "Separates binding affinity, functional potency and response magnitude." }, { "name": "Channel kinetics", "kind": "measurement", "unit_or_values": "Activation, deactivation, desensitization and recovery times in ms or s", "why_it_matters": "Determines how stimulus duration and repetition affect the observed response." }, { "name": "Ion conduction", "kind": "measurement", "unit_or_values": "Conductance in pS, reversal potential in mV, relative permeability ratios and current-voltage relation", "why_it_matters": "Characterizes charge transport without assigning one conductance or calcium permeability to the entire family." }, { "name": "Experimental preparation", "kind": "relation", "unit_or_values": "Native tissue or recombinant system, organism, cell type and recording protocol", "why_it_matters": "Defines the context in which a receptor property was established." } ], "affordances": [ "Resolve historical subunit names to current GluK identities while retaining the original terminology.", "Assess whether a proposed subunit combination has evidence for functional assembly.", "Compare receptor responses after matching composition, auxiliary proteins and assay conditions.", "Select binding or electrophysiological measurements appropriate to the unresolved receptor property.", "Evaluate agonist, antagonist or genetic perturbations for their ability to distinguish kainate-receptor effects.", "Flag unsupported transfers from recombinant assemblies to native receptor populations." ], "agent_conduct": { "may": [ "Explain the structure and roles of kainate receptors from scientific sources.", "Summarise research on these receptors with citations." ], "must_not": [ "Recommend compounds acting on these receptors for personal use.", "Present early research as proven treatment for epilepsy or pain.", "Interpret a person's genetic test on a receptor gene as a diagnosis.", "Assist in making or using neurotoxins that act on these receptors to harm people or animals." ], "requires_human": [ "Using receptor research in decisions about patient treatment." ] }, "ethics": { "considerations": [ "Brain research can lead to treatments but also to harmful substances; dual use needs care.", "Animal research on seizures raises welfare questions." ], "affected_parties": [ "Patients with epilepsy and neurological conditions", "Laboratory animals", "Research participants" ] }, "owners": { "steward": "Nobody owns the receptors; researchers answer for their data.", "master_systems": [ "Protein and gene databases" ] }, "failure_modes_and_hazards": [ "Overactivation of these receptors is linked to seizures and nerve cell damage.", "Naturally occurring toxins acting on related receptors can contaminate shellfish." ], "standards_and_regulation": [ "IUPHAR/BPS receptor nomenclature, International Union of Basic and Clinical Pharmacology." ], "what_it_is_for": [ "Kainate receptors occur in neuronal membranes, where they contribute to excitatory signaling and regulation of synaptic transmission.", "They are studied in neuroscience and pharmacology to relate receptor composition to ion currents, synaptic function and neurological disease." ], "visual_identification": [ "Resolved molecular structures show four subunits surrounding a central membrane-spanning ion pore, a feature shared with other ionotropic glutamate receptors.", "Extracellular amino-terminal and ligand-binding domains form a layered assembly above the membrane-spanning region.", "Assignment to the kainate receptor class requires identification of GluK1-GluK5 subunits because overall molecular shape alone does not reliably distinguish related receptor classes." ] }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q3454536: kainate receptor", "url": "https://www.wikidata.org/wiki/Q3454536", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Kainate receptor", "url": "https://en.wikipedia.org/wiki/Kainate_receptor", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "molecular-identity-and-assembly", "name": "Molecular identity and assembly", "description": "Identify the receptor population through its constituent proteins and their assembled configuration.", "rationale": "The family name alone does not specify which molecular receptor produced a result.", "layers": [ { "id": "subunit-identity", "name": "Subunit identity", "description": "Resolve species, nomenclature and sequence variants.", "findings": [ { "id": "resolved-gluk-components", "name": "Resolved GluK components", "description": "Record current subunit names alongside accessions and historical labels. Human GluK1 corresponds to GRIK1. [IUPHAR/BPS GluK1](https://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId=450)", "questions": [ { "text": "Which GluK subunits, species and accessions identify the receptor under consideration?", "kind": "definition", "id": "resolved-gluk-components-q01" }, { "text": "Which splice forms, editing states or engineered sequence changes were established in the preparation?", "kind": "provenance", "id": "resolved-gluk-components-q02" } ] } ] }, { "id": "assembly-resolution", "name": "Assembly resolution", "description": "Separate detected components from demonstrated co-assembly.", "findings": [ { "id": "functional-complex-evidence", "name": "Functional complex evidence", "description": "Record homomeric or heteromeric assignment, proposed stoichiometry and evidence that the components form the same functional complex.", "questions": [ { "text": "What evidence distinguishes co-assembly from subunits merely being expressed in the same cell?", "kind": "provenance", "id": "functional-complex-evidence-q01" }, { "text": "Does the observation describe an isolated subunit, one receptor assembly or a mixture of receptor populations?", "kind": "boundary", "id": "functional-complex-evidence-q02" } ] } ] } ] }, { "id": "membrane-context-and-partners", "name": "Membrane context and partners", "description": "Describe where the receptor is available and which proteins accompany it.", "rationale": "Expression, surface delivery and localization support different claims about receptor function.", "layers": [ { "id": "surface-availability", "name": "Surface availability", "description": "Distinguish total receptor material from receptors delivered to the plasma membrane.", "findings": [ { "id": "surface-delivery-evidence", "name": "Surface delivery evidence", "description": "Track total abundance and surface abundance separately; ligand-binding-site mutations have affected expression and surface delivery in recombinant kainate-receptor experiments. [Primary study](https://pubmed.ncbi.nlm.nih.gov/30302614/)", "questions": [ { "text": "Which assay establishes plasma-membrane availability rather than total cellular subunit abundance?", "kind": "measurement", "id": "surface-delivery-evidence-q01" }, { "text": "Could a reduced response reflect impaired surface delivery, and what measurement would distinguish it from altered gating?", "kind": "action", "id": "surface-delivery-evidence-q02" } ] } ] }, { "id": "local-environment", "name": "Local environment", "description": "Specify cellular compartment and associated proteins.", "findings": [ { "id": "compartment-and-auxiliary-context", "name": "Compartment and auxiliary context", "description": "Record presynaptic, postsynaptic or other localization and whether NETO-family or other partners were tested, detected or experimentally supplied.", "questions": [ { "text": "What evidence places this receptor population in the stated cell type and membrane compartment?", "kind": "provenance", "id": "compartment-and-auxiliary-context-q01" }, { "text": "Which auxiliary proteins are present, and is their association with this receptor demonstrated or assumed?", "kind": "provenance", "id": "compartment-and-auxiliary-context-q02" } ] } ] } ] }, { "id": "gating-and-ion-permeation", "name": "Gating and ion permeation", "description": "Describe stimulus-dependent channel states and the ion flow they permit.", "rationale": "A receptor's response depends on both state transitions and permeation properties.", "layers": [ { "id": "activation-and-desensitization", "name": "Activation and desensitization", "description": "Resolve the time course of opening, response decay and recovery.", "findings": [ { "id": "stimulus-linked-state-transitions", "name": "Stimulus-linked state transitions", "description": "Associate kinetic measurements with ligand identity, concentration, application speed and pulse history instead of treating response amplitude as a complete functional description.", "questions": [ { "text": "What ligand pulse and solution-exchange conditions produced the measured activation and desensitization?", "kind": "measurement", "id": "stimulus-linked-state-transitions-q01" }, { "text": "What paired-pulse or washout experiment distinguishes desensitization from persistent blockade or receptor loss?", "kind": "action", "id": "stimulus-linked-state-transitions-q02" } ] } ] }, { "id": "conductance-and-selectivity", "name": "Conductance and selectivity", "description": "Connect ion transport measurements to receptor composition and recording conditions.", "findings": [ { "id": "variant-dependent-permeation", "name": "Variant-dependent permeation", "description": "Retain editing and assembly context when recording channel conductance; recombinant experiments demonstrate dependence on Q/R editing and subunit co-assembly. [Primary study](https://pubmed.ncbi.nlm.nih.gov/8730589/)", "questions": [ { "text": "What conductance, reversal potential and permeability measurements were obtained, with which ionic solutions and voltages?", "kind": "measurement", "id": "variant-dependent-permeation-q01" }, { "text": "Were relevant editing states determined directly, and how do they limit interpretation of calcium permeability or rectification?", "kind": "boundary", "id": "variant-dependent-permeation-q02" } ] } ] } ] }, { "id": "pharmacology-and-functional-attribution", "name": "Pharmacology and functional attribution", "description": "Relate experimental perturbations to receptor-specific effects with explicit limits.", "rationale": "Ligand responses and downstream changes require controls before they can identify a kainate-receptor mechanism.", "layers": [ { "id": "ligand-response", "name": "Ligand response", "description": "Distinguish binding, activation, inhibition and modulation.", "findings": [ { "id": "assay-qualified-pharmacology", "name": "Assay-qualified pharmacology", "description": "Record ligand identity, concentration range, assay endpoint and receptor composition; keep binding affinity distinct from functional potency and efficacy.", "questions": [ { "text": "Does the reported parameter measure binding, peak current, steady-state current or a downstream endpoint?", "kind": "definition", "id": "assay-qualified-pharmacology-q01" }, { "text": "Which selectivity controls distinguish this ligand's kainate-receptor effect from activity at neighbouring glutamate receptors?", "kind": "action", "id": "assay-qualified-pharmacology-q02" } ] } ] }, { "id": "causal-attribution", "name": "Causal attribution", "description": "Separate receptor-level observations from cellular and circuit interpretations.", "findings": [ { "id": "mechanism-and-transfer-limits", "name": "Mechanism and transfer limits", "description": "Attach pharmacological, genetic and recording evidence to each functional claim, identifying whether it supports direct channel current, an indirect response or a proposed non-ionotropic mechanism.", "questions": [ { "text": "Which independent controls establish that the observed effect depends on the identified kainate receptor population?", "kind": "provenance", "id": "mechanism-and-transfer-limits-q01" }, { "text": "What evidence separates ion flux through the receptor from downstream signalling or network-mediated effects?", "kind": "boundary", "id": "mechanism-and-transfer-limits-q02" }, { "text": "Which preparation differences must be resolved before transferring this finding to native tissue?", "kind": "action", "id": "mechanism-and-transfer-limits-q03" } ] } ] } ] }, { "id": "evidence-and-external-alignment", "name": "Evidence and external alignment", "description": "What the world already says about this thing, gathered so the model can be checked against it.", "rationale": "A model that cannot be lined up against existing standards, identifiers and practice cannot be adopted by anyone who already uses them.", "layers": [ { "id": "reported-evidence", "name": "Reported evidence", "description": "Findings from the breadth pass, kept separate from the structural claims.", "findings": [ { "id": "evidence-confidence-notes", "name": "Check these first", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "The name denotes a receptor family rather than a single chemical substance; a universal CAS number, purity specification or melting point would be inappropriate.", "GluK4 and GluK5 require coassembly with GluK1, GluK2 or GluK3 to form functional channels.", "Quantitative kinetics, conductance, agonist potency and calcium permeability require a specified species, subunit composition, editing state and experimental protocol; no sources were consulted for this recall." ], "questions": [ { "id": "evidence-confidence-notes-q01", "text": "Which of these check these first hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-kinds", "name": "Kinds and varieties", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Homomeric receptors assembled from GluK1, GluK2 or GluK3", "Heteromeric receptors combining GluK1-GluK3 subunits", "Heteromeric receptors incorporating GluK4 or GluK5 together with GluK1-GluK3" ], "questions": [ { "id": "evidence-kinds-q01", "text": "Which of these kinds and varieties hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-identifiers", "name": "Identifiers and schemes", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "scheme": "IUPHAR receptor nomenclature", "value_or_pattern": "GluK1, GluK2, GluK3, GluK4, GluK5", "note": "These designate subunits, not five uniquely defined assembled receptors; older names are GluR5, GluR6, GluR7, KA1 and KA2, respectively." }, { "scheme": "HGNC approved human gene symbols", "value_or_pattern": "GRIK1, GRIK2, GRIK3, GRIK4, GRIK5", "note": "These genes encode the corresponding GluK1-GluK5 subunits; gene identifiers should not be treated as identifiers for assembled receptor complexes." } ], "questions": [ { "id": "evidence-identifiers-q01", "text": "Which of these identifiers and schemes hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-real-world-use", "name": "Real-world use", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Experimental investigation of excitatory synaptic transmission, synaptic plasticity and presynaptic regulation of neurotransmitter release.", "Pharmacological studies using kainate receptor agonists and antagonists to investigate receptor function.", "Research into seizure mechanisms and excitotoxic neuronal injury." ], "questions": [ { "id": "evidence-real-world-use-q01", "text": "Which of these real-world use hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-measurements", "name": "Typical measurements", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "quantity": "Number of subunits in an assembled receptor", "typical_range": "4", "unit": "subunits" } ], "questions": [ { "id": "evidence-measurements-q01", "text": "Which of these typical measurements hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-failure-modes-and-hazards", "name": "Failure modes and hazards", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ "Excessive activation can contribute to neuronal hyperexcitability, seizures and excitotoxic injury.", "Rapid desensitization can reduce current during sustained agonist exposure and complicate functional measurements.", "Subunit composition and RNA editing affect channel properties, including calcium permeability, so results cannot be generalized across all kainate receptors.", "Kainate can also activate AMPA receptors; responses to kainate alone do not establish kainate receptor involvement." ], "questions": [ { "id": "evidence-failure-modes-and-hazards-q01", "text": "Which of these failure modes and hazards hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] }, { "id": "evidence-neighbours", "name": "Neighbouring kinds and how to tell them apart", "description": "Recalled without web access and unsourced; every item is a lead to verify.", "evidence": [ { "name": "AMPA receptor", "difference": "A related ionotropic glutamate receptor assembled from GluA1-GluA4 rather than GluK1-GluK5 subunits." }, { "name": "NMDA receptor", "difference": "A distinct ionotropic glutamate receptor family with characteristic co-agonist requirements and voltage-dependent magnesium block." }, { "name": "Metabotropic glutamate receptor", "difference": "A G protein-coupled glutamate receptor rather than a glutamate-gated ion channel." }, { "name": "Kainic acid", "difference": "A small-molecule agonist after which the receptor is named, rather than the receptor protein complex." } ], "questions": [ { "id": "evidence-neighbours-q01", "text": "Which of these neighbouring kinds and how to tell them apart hold for the sense of kainate receptor this model covers, and on what evidence?", "kind": "provenance" } ] } ] } ] } ] }, "openQuestions": [ "Does the registry intend this entry to cover all taxonomic kainate-receptor homologues, or primarily the vertebrate GluK1-GluK5 family?", "Which native subunit stoichiometries are directly established for the cell types of interest, and which remain inferred from expression?", "How completely are editing states, splice variants and auxiliary-protein associations characterized in the intended preparations?", "Which reported non-ionotropic effects have evidence that separates them from ion conduction and indirect network activity?", "Which ligand and genetic-control combinations provide adequate receptor attribution in the intended experimental system?" ], "statistics": { "bundles": 5, "layers": 9, "findings": 15, "questions": 24 } }